A genomic perspective on cryptic species reveals complex evolutionary dynamics in the gray zone of the speciation continuum

The evolutionary dynamics of cryptic species remain poorly understood, and their detection relies primarily on methods that quantify divergence, assuming that gene flow is absent. Here, we examine how gene flow shapes the evolutionary trajectories and species boundaries in Bornean Fanged Frogs, a renowned example of cryptic diversity where a single species has been split into 18 genetically divergent yet morphologically indistinguishable species. We employed target-capture data from over 13,000 loci to assess lineage independence of 14 nominal species distributed across Malaysian Borneo by evaluating both divergence and cohesion using network multispecies coalescent (NMSC) and MSC + migration approaches. Under the Unified Species Concept, only six of the 14 nominal species unambiguously form independently evolving lineages; the remainder represent cohesive metapopulation lineages nested within those six species. While mitochondrial p-distances varied substantially (up to 10%), genome-wi..., , # Data from: A genomic perspective on cryptic species reveals complex evolutionary dynamics in the gray zone of the speciation continuum

Dataset DOI: [10.5061/dryad.c866t1gk6](https://doi.org/10.5061/dryad.c866t1gk6)

## Description of the data and file structure

All data relevant to the reproducibility of this study are made available, including **sequence alignments** (16S and genomic), **pairwise p-distance calculations**, raw results from the **pixy analysis** (Dxy, Fst, and pi), **SNP dataset** in STRUCTURE format, and **phylogenetic trees** (species, gene, and consensus trees).

### Files and variables

#### File: scripts_others.zip

**Description:** Various helper bash and Python scripts:\
**filter_alignments.sh:** subsets alignment files based on a predefined list of loci. It reads locus IDs from a text file and copies the corresponding `.phy` alignment files from a source directory into a new directory for downstream phylogenetic analyses.

**filter_genetrees.sh:** subsets a ...,